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    Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons

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    Author
    Kronman, Hope
    Richter, Felix
    Labonté, Benoit
    Chandra, Ramesh
    Date
    2019-05-24
    Journal
    Scientific Reports
    Publisher
    Nature Publishing Group
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://dx.doi.org/10.1038/s41598-019-44798-9
    Abstract
    Subcellular RNAseq promises to dissect transcriptional dynamics but is not well characterized. Furthermore, FACS may introduce bias but has not been benchmarked genome-wide. Finally, D1 and D2 dopamine receptor-expressing medium spiny neurons (MSNs) of the nucleus accumbens (NAc) are fundamental to neuropsychiatric traits but have only a short list of canonical surface markers. We address these gaps by systematically comparing nuclear-FACS, whole cell-FACS, and RiboTag affinity purification from D1- and D2-MSNs. Using differential expression, variance partitioning, and co-expression, we identify the following trade-offs for each method. RiboTag-seq best distinguishes D1- and D2-MSNs but has the lowest transcriptome coverage. Nuclear-FACS-seq generates the most differentially expressed genes and overlaps significantly with neuropsychiatric genetic risk loci, but un-annotated genes hamper interpretation. Whole cell-FACS is more similar to nuclear-FACS than RiboTag, but captures aspects of both. Using pan-method approaches, we discover that transcriptional regulation is predominant in D1-MSNs, while D2-MSNs tend towards cytosolic regulation. We are also the first to find evidence for moderate sexual dimorphism in these cell types at baseline. As these results are from 49 mice (nmale = 39, nfemale = 10), they represent generalizable ground-truths. Together, these results guide RNAseq methods selection, define MSN transcriptomes, highlight neuronal sex differences, and provide a baseline for D1- and D2-MSNs. © 2019, The Author(s).
    Description
    All data are available on NCBI’s GEO database, and can be found under the Accession Number GSE121199.
    Sponsors
    National Institute on Drug Abuse (NIDA) P01DA008227; National Institute of Mental Health (NIMH) P50MH096890
    Keyword
    medium spiny neurons
    fluorescence-activated cell sorting
    Sequence Analysis, RNA
    Cell Separation
    Nucleus Accumbens
    Ventral Striatum
    Identifier to cite or link to this item
    https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85066927652&origin=inward; http://hdl.handle.net/10713/9561
    ae974a485f413a2113503eed53cd6c53
    10.1038/s41598-019-44798-9
    Scopus Count
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